sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities are compared using Shaper.
For more information, please see the following publication:
Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 3w3k | L07 | Toll-like receptor 8 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3w3k | L07 | Toll-like receptor 8 | / | 1.000 | |
| 3w3l | RX8 | Toll-like receptor 8 | / | 0.595 | |
| 3w3n | RX8 | Toll-like receptor 8 | / | 0.585 | |
| 4r09 | URI | Toll-like receptor 8 | / | 0.540 | |
| 4r08 | URI | Toll-like receptor 8 | / | 0.533 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.522 | |
| 4r07 | URI | Toll-like receptor 8 | / | 0.521 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.492 | |
| 1jdz | FMB | Purine nucleoside phosphorylase | / | 0.491 | |
| 4fgc | PQ0 | NADPH-dependent 7-cyano-7-deazaguanine reductase | 1.7.1.13 | 0.489 | |
| 2j0s | ANP | Eukaryotic initiation factor 4A-III | 3.6.4.13 | 0.488 | |
| 3ge7 | AFQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.472 | |
| 2flh | ZEA | Cytokinin-specific binding protein | / | 0.471 | |
| 4iyg | 1HU | Strictosidine synthase | 4.3.3.2 | 0.470 | |
| 3nmh | PYV | Abscisic acid receptor PYL2 | / | 0.469 | |
| 2c1b | CQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.468 | |
| 2zu9 | GDP | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.467 | |
| 1jdv | ADN | Purine nucleoside phosphorylase | / | 0.466 | |
| 3py4 | TYL | Lactoperoxidase | 1.11.1.7 | 0.466 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 3bt9 | DEQ | HTH-type transcriptional regulator QacR | / | 0.463 | |
| 4fr1 | 0V2 | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.462 | |
| 1qvt | PRL | HTH-type transcriptional regulator QacR | / | 0.461 | |
| 2oal | FAD | Flavin-dependent tryptophan halogenase RebH | 1.14.19.9 | 0.458 | |
| 1jdt | MTA | Purine nucleoside phosphorylase | / | 0.457 | |
| 1pr5 | TBN | Purine nucleoside phosphorylase DeoD-type | / | 0.457 | |
| 4y6n | UPG | Glucosyl-3-phosphoglycerate synthase | 2.4.1.266 | 0.456 | |
| 4h1e | 10J | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 1je1 | GMP | Purine nucleoside phosphorylase | / | 0.453 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.453 | |
| 3vv8 | B02 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 4h0u | UMP | Thymidylate synthase | / | 0.453 | |
| 4y9x | UPG | Glucosyl-3-phosphoglycerate synthase | 2.4.1.266 | 0.453 | |
| 1n77 | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.452 | |
| 2ojf | 4PY | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.451 | |
| 2wvl | GDD | Mannosyl-3-phosphogylcerate synthase | / | 0.451 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.450 | |
| 2jds | L20 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.450 | |
| 2pot | GUN | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.450 | |
| 4jxx | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.450 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.449 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 4djw | 0KP | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4id9 | NAD | Putative UDP-glucose 4-epimerase | / | 0.448 | |
| 3rme | RME | Acidic mammalian chitinase | 3.2.1.14 | 0.447 | |
| 4lrr | CF9 | Thymidylate synthase | / | 0.447 | |
| 1gvv | 0GM | Endothiapepsin | 3.4.23.22 | 0.446 | |
| 2re8 | GSU | Glutamine--tRNA ligase | 6.1.1.18 | 0.446 | |
| 2zu8 | GDD | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.446 | |
| 3anl | SYC | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.446 | |
| 3aw9 | GDU | NAD-dependent epimerase/dehydratase | / | 0.446 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.446 | |
| 3isj | A8D | Pantothenate synthetase | 6.3.2.1 | 0.446 | |
| 4aox | FAD | Steroid monooxygenase | / | 0.445 | |
| 4jq8 | KJ8 | Epidermal growth factor receptor | 2.7.10.1 | 0.445 | |
| 2oa1 | FAD | Flavin-dependent tryptophan halogenase RebH | 1.14.19.9 | 0.444 | |
| 3arq | DM5 | Chitinase A | / | 0.444 | |
| 3b4p | 3B4 | Phenazine biosynthesis protein A/B | / | 0.444 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.444 | |
| 3ivg | FG5 | Pantothenate synthetase | 6.3.2.1 | 0.444 | |
| 3uxv | GUN | NADPH-dependent 7-cyano-7-deazaguanine reductase | / | 0.444 | |
| 4mk8 | 28Q | Genome polyprotein | 2.7.7.48 | 0.444 | |
| 4x7u | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.444 | |
| 2b35 | TCL | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 2rd6 | 78P | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.443 | |
| 2y02 | WHJ | Beta-1 adrenergic receptor | / | 0.443 | |
| 3wb4 | 0B3 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 1efy | BZC | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.442 | |
| 2acw | UPG | Glycosyltransferase | / | 0.442 | |
| 4u7w | NDP | MxaA | / | 0.442 | |
| 1gax | VAA | Valine--tRNA ligase | 6.1.1.9 | 0.441 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 3wd3 | A1L | Chitinase B | 3.2.1.14 | 0.441 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4c35 | NU3 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 4ej4 | EJ4 | Delta-type opioid receptor | / | 0.441 | |
| 1qtq | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.440 | |
| 4gi4 | 0EX | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.440 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.440 |